Re: Nonlinear transform EPI data

Hi Rick,

I have a relevant question here. Actually, what I want to do is to nonlinearly-warp back the data from the standard space to individual native space. For example, I would like to obtain a set of masks (i.e., atlas) in each individual’s native space. Those masks have been registered to a template in standard space. I used to warp a subject’s structural image to a template: -base template_t1.nii -input subject_t1.nii -skull_strip_input yes

Then, I consider using 3dNwarpApply with -iwarp option as follow:

3dNwarpApply -master subject_t1.nii -dxyz 2 -source atlas_masks.nii -iwarp -nwarp ‘anat.un.aff.qw_WARP.nii anat.un.aff.nii.Xaff.1D’ -ainterp NN -prefix atlas_native_space.nii

I am not sure if I understand option -iwarp correctly, but the result given by script above does not match the subject_t1 image. Actually, it is far away from the subject_t1 image. Could you help to take a look at if this script is the correct way to do this? If not, how can I achieve my goal (i.e., warp-back the masks from standard space to native space according to the nonlinear transformation of subject’s t1 to the template)? Thanks!



This question was originally asked on a separate existing thread, and was split into its own since it is a different topic. Because there were two starting points to the thread, to avoid confusion this question has been merged with the clarifying point here:,160926,160926#msg-160926

and so all discussions about this point should be carried on there.